6-32754409-C-A

Variant names:

• chr6-32754409-C-A
• rs10807113

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.499 in 151,918 control chromosomes in the GnomAD database, including 19,766 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75671 AN: 151800 Hom.: 19736 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.499 AC: 75761 AN: 151918 Hom.: 19766 Cov.: 32 AF XY: 0.509 AC XY: 37757 AN XY: 74248

African (AFR) AF: 0.389 AC: 16133 AN: 41420

American (AMR) AF: 0.553 AC: 8444 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1930 AN: 3460

East Asian (EAS) AF: 0.809 AC: 4191 AN: 5178

South Asian (SAS) AF: 0.682 AC: 3280 AN: 4806

European-Finnish (FIN) AF: 0.577 AC: 6090 AN: 10560

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33767 AN: 67918

Other (OTH) AF: 0.528 AC: 1114 AN: 2108

Alfa AF: 0.488 Hom.: 48456

Bravo AF: 0.491

Asia WGS AF: 0.693 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.0070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10807113; hg19: chr6-32722186;